Directly, no. The AKAIO team has not added that ability. If you have a GBA Gameshark or other cheating device, you can use GBA ExpLoader to flash the game to the 3in1 and then use the cheat device. The only other way is to hack/patch the game with Ez-Flash 4 (I think) so that the cheats are hardcoded into the game. Keep a backup of the game so that you can always go back to normal.
Check out how_do_i_do_that's signature. He has a link in it to a FAQ about GBA "adapters".